Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013568.1 Corchorus olitorius cultivar O-4 contig13601, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12922
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:2302 original size:76 final size:76
Alignment explanation
Indices: 2167--2308 Score: 173
Period size: 76 Copynumber: 1.9 Consensus size: 76
2157 AAGGACCCCG
* * *
2167 ACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGGACCCAGGTGG
1 ACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGATGG
2232 GCAGTGTCACA
66 GCAGTGTCACA
* * * *
2243 ACTCCAGCTGGGTGCCCACATGGTTTG-TTTGAAG-ACCCATGT-GTTTCGCCTGATCACCCAGA
1 ACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGCACCCAGA
2305 TGGG
63 TGGG
2309 TTGTTTCATA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
75 4 0.07
76 47 0.84
77 5 0.09
ACGTcount: A:0.18, C:0.29, G:0.29, T:0.25
Consensus pattern (76 bp):
ACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGATGG
GCAGTGTCACA
Found at i:4526 original size:42 final size:40
Alignment explanation
Indices: 4414--4556 Score: 115
Period size: 40 Copynumber: 3.5 Consensus size: 40
4404 TTATTGTATG
* * *
4414 ATGCAATTTTGTCCCTGATTTAGGATTTTATTTTTAATTT
1 ATGCAATTTAGTCCCTGATTTAGGATTTTATTTCTAATTA
**** * *
4454 ATGCGGCCTAGTCCCTGATTTAAGACTTTATTTCCTAATTAA
1 ATGCAATTTAGTCCCTGATTTAGGATTTTATTT-CTAATT-A
* * * ** *
4496 ATGCAATTTGGTCCCTGCTTTAGGATTTTATTTATTTTTG
1 ATGCAATTTAGTCCCTGATTTAGGATTTTATTTCTAATTA
* *
4536 ATGCAATTTAATCCCTTATTT
1 ATGCAATTTAGTCCCTGATTT
4557 TAGAAATTGA
Statistics
Matches: 76, Mismatches: 25, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
40 43 0.57
41 8 0.11
42 25 0.33
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.48
Consensus pattern (40 bp):
ATGCAATTTAGTCCCTGATTTAGGATTTTATTTCTAATTA
Found at i:8628 original size:21 final size:21
Alignment explanation
Indices: 8604--8644 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
8594 TTTTATTAAC
8604 TTCCAAAATCTTCTTTTGGAT
1 TTCCAAAATCTTCTTTTGGAT
8625 TTCCAAAATCTTCTTTTGGA
1 TTCCAAAATCTTCTTTTGGA
8645 ATTATCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (21 bp):
TTCCAAAATCTTCTTTTGGAT
Found at i:8662 original size:31 final size:30
Alignment explanation
Indices: 8624--8683 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 30
8614 TTCTTTTGGA
8624 TTTCCAAAATCTTCTTTTGGAATTATCTTAT
1 TTTCCAAAATCTTCTTTTGGAATTA-CTTAT
*
8655 TTTCCAAAATCTTCTTTTGGATTTACTTA
1 TTTCCAAAATCTTCTTTTGGAATTACTTA
8684 AGAAAAGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.52
Consensus pattern (30 bp):
TTTCCAAAATCTTCTTTTGGAATTACTTAT
Found at i:8672 original size:15 final size:15
Alignment explanation
Indices: 8624--8672 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
8614 TTCTTTTGGA
8624 TTTCCAAAATCTTCT
1 TTTCCAAAATCTTCT
** * *
8639 TTTGGAATTATCTTAT
1 TTTCCAA-AATCTTCT
8655 TTTCCAAAATCTTCT
1 TTTCCAAAATCTTCT
8670 TTT
1 TTT
8673 GGATTTACTT
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.24, C:0.18, G:0.04, T:0.53
Consensus pattern (15 bp):
TTTCCAAAATCTTCT
Found at i:10544 original size:836 final size:836
Alignment explanation
Indices: 8932--10598 Score: 3165
Period size: 836 Copynumber: 2.0 Consensus size: 836
8922 AAAGCACTTC
* *
8932 CCAGGATATATATTCGGAGCCCCAACGCATCCCGAGAAGAGCCGTCTCATCCTCGGAGACATTCA
1 CCAGGATATATACTCGGAGCCCCAACGCATCCCGAGAAGAGCCGTCTCATCCCCGGAGACATTCA
*
8997 GTGGCCCCGAAAACTCGACCACTCACTGAATGCCCCTTCTTCGGAAGGGTTACGGTCATTAACTG
66 GTGGCCCCGAAAACTCGACCACTCACTGAATGCCCCTTCTTCGAAAGGGTTACGGTCATTAACTG
9062 AATTTAAAAGGTGGCATGTAATGCAAACAGATACAATCAATGACAGGTAAATATGATATGCATGC
131 AATTTAAAAGGTGGCATGTAATGCAAACAGATACAATCAATGACAGGTAAATATGATATGCATGC
*
9127 AACTAAGTTCTATTTTAGCACTACTCTAAATTACTAAATTACTACAAACCAAGGCCCGATTGGAC
196 AACTAAGTTCTACTTTAGCACTACTCTAAATTACTAAATTACTACAAACCAAGGCCCGATTGGAC
9192 CAAATAACAAATTAACAATAATTAAAGAGAAATAAAAACTTATGGGCCGGACTAGGCATACTGGG
261 CAAATAACAAATTAACAATAATTAAAGAGAAATAAAAACTTATGGGCCGGACTAGGCATACTGGG
*
9257 AACCTTTCTACACACTAAAGAAAACGATTAGTGAAATTCAGGAAGCAAATAAAACAAATTACACC
326 AACCTTTCTACACACTAAAGAAAACGATCAGTGAAATTCAGGAAGCAAATAAAACAAATTACACC
* *
9322 TTCACAATGCAAGTCAAGTATCAAAATTCACCAAGTAGCAACCATAATTTGGAATTAAAGTCATC
391 TTCACAATGCAAGTCAAGAATCAAAATTCACCAAGTAGCAACCATAATTAGGAATTAAAGTCATC
*
9387 ATGGAGATAACTCAACCTTTAAACAAATAAGAATGCTAATCACACCACATTGGAATTCAATGAAA
456 ATGGAGATAACTCAACCTTTAAACAAATAAGAATGCAAATCACACCACATTGGAATTCAATGAAA
9452 ATCATCTTAAAGAAAACTAGCTCTTACACCCAAAATCTCAATTCTCAACTTAGAATCAAATCATA
521 ATCATCTTAAAGAAAACTAGCTCTTACACCCAAAATCTCAATTCTCAACTTAGAATCAAATCATA
9517 GGAATTTGTCAATTTCCTTTCAAATTAATCTCAATTTGAGAAATTAGGTCTTTAACTCCAAGTTT
586 GGAATTTGTCAATTTCCTTTCAAATTAATCTCAATTTGAGAAATTAGGTCTTTAACTCCAAGTTT
*
9582 AACTTCCTTAAAATTAAAATTAGCCCGAAGTGTCTTATCATATCATCTTCAAGCTAACTCTAATT
651 AACTTCCTTAAAATTAAAATTAGACCGAAGTGTCTTATCATATCATCTTCAAGCTAACTCTAATT
* *
9647 TTAAGAAAATCTTCACTTTAAGTTAAGACCCCATTTCCAAATCAAGATTAGTTTAATTAGAAATC
716 TTAAAAAAATCTTCACTTTAAGTAAAGACCCCATTTCCAAATCAAGATTAGTTTAATTAGAAATC
9712 AAAAGCTAGAATCCAATATCAATTTAGCTCTTAAGAATTAGTTACCACAAACTCGA
781 AAAAGCTAGAATCCAATATCAATTTAGCTCTTAAGAATTAGTTACCACAAACTCGA
* * *
9768 CCAGGATATATGCTCGGAGCCCCGACGCATCCCGAGAAGAGTCGTCTCATCCCCGGAGACATTCA
1 CCAGGATATATACTCGGAGCCCCAACGCATCCCGAGAAGAGCCGTCTCATCCCCGGAGACATTCA
9833 GTGGCCCCGAAAACTCGACCACTCACTGAATGCCCCTTCTTCGAAAGGGTTACGGTCATTAACTG
66 GTGGCCCCGAAAACTCGACCACTCACTGAATGCCCCTTCTTCGAAAGGGTTACGGTCATTAACTG
*
9898 AATTTAAAAGGTGGCATGTAATGCAAACAGATACAATCAATGGCAGGTAAATATGATATGCATGC
131 AATTTAAAAGGTGGCATGTAATGCAAACAGATACAATCAATGACAGGTAAATATGATATGCATGC
9963 AACTAAGTTCTACTTTAGCACTACTCTAAATTACTAAATTACTACAAACCAAGGCCCGATTGGAC
196 AACTAAGTTCTACTTTAGCACTACTCTAAATTACTAAATTACTACAAACCAAGGCCCGATTGGAC
10028 CAAATAACAAATTAACAATAATTAAAGAGAAATAAAAACTTATGGGCCGGACTAGGCATACTGGG
261 CAAATAACAAATTAACAATAATTAAAGAGAAATAAAAACTTATGGGCCGGACTAGGCATACTGGG
10093 AACCTTTCTACACACTAAAGAAAACGATCAGTGAAATAT-AGGAAGCAAATAAAACAAATTACAC
326 AACCTTTCTACACACTAAAGAAAACGATCAGTGAAAT-TCAGGAAGCAAATAAAACAAATTACAC
10157 CTTCACAATGCAAGTCAAGAATCAAAATTCACCAAGTAGCAACCATAATTAGGAATTAAAGTCAT
390 CTTCACAATGCAAGTCAAGAATCAAAATTCACCAAGTAGCAACCATAATTAGGAATTAAAGTCAT
*
10222 CATGGAGATAACTCAACCTTTAAACAAATAAGAATGCAAATCACAGCACATTGGAATTCAATGAA
455 CATGGAGATAACTCAACCTTTAAACAAATAAGAATGCAAATCACACCACATTGGAATTCAATGAA
10287 AATCATCTTAAAGAAAACTAGCTCTTACACCCAAAATCTCAATTCTCAACTTAGAATCAAATCAT
520 AATCATCTTAAAGAAAACTAGCTCTTACACCCAAAATCTCAATTCTCAACTTAGAATCAAATCAT
10352 AGGAATTTGTCAATTTCCTTTCAAATTAATCTCAATTTGAGAAATTAGGTCTTTAACTCCAAGTT
585 AGGAATTTGTCAATTTCCTTTCAAATTAATCTCAATTTGAGAAATTAGGTCTTTAACTCCAAGTT
10417 TAACTTCCTTAAAATTAAAATTAGACCGAAGTGTCTTATCATATCATCTTCAAGCTAACTCTAAT
650 TAACTTCCTTAAAATTAAAATTAGACCGAAGTGTCTTATCATATCATCTTCAAGCTAACTCTAAT
*
10482 TTTAAAAAAATCTTCACTTTAGGTAAAGACCCCATTTCCAAATCAAGATTAGTTTAATTAGAAAT
715 TTTAAAAAAATCTTCACTTTAAGTAAAGACCCCATTTCCAAATCAAGATTAGTTTAATTAGAAAT
10547 CAAAAGCTAGAATCCAATATCAATTTAGCTCTTAAGAATTAGTTACCACAAA
780 CAAAAGCTAGAATCCAATATCAATTTAGCTCTTAAGAATTAGTTACCACAAA
10599 TGAACAAATC
Statistics
Matches: 813, Mismatches: 17, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
836 812 1.00
837 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.27
Consensus pattern (836 bp):
CCAGGATATATACTCGGAGCCCCAACGCATCCCGAGAAGAGCCGTCTCATCCCCGGAGACATTCA
GTGGCCCCGAAAACTCGACCACTCACTGAATGCCCCTTCTTCGAAAGGGTTACGGTCATTAACTG
AATTTAAAAGGTGGCATGTAATGCAAACAGATACAATCAATGACAGGTAAATATGATATGCATGC
AACTAAGTTCTACTTTAGCACTACTCTAAATTACTAAATTACTACAAACCAAGGCCCGATTGGAC
CAAATAACAAATTAACAATAATTAAAGAGAAATAAAAACTTATGGGCCGGACTAGGCATACTGGG
AACCTTTCTACACACTAAAGAAAACGATCAGTGAAATTCAGGAAGCAAATAAAACAAATTACACC
TTCACAATGCAAGTCAAGAATCAAAATTCACCAAGTAGCAACCATAATTAGGAATTAAAGTCATC
ATGGAGATAACTCAACCTTTAAACAAATAAGAATGCAAATCACACCACATTGGAATTCAATGAAA
ATCATCTTAAAGAAAACTAGCTCTTACACCCAAAATCTCAATTCTCAACTTAGAATCAAATCATA
GGAATTTGTCAATTTCCTTTCAAATTAATCTCAATTTGAGAAATTAGGTCTTTAACTCCAAGTTT
AACTTCCTTAAAATTAAAATTAGACCGAAGTGTCTTATCATATCATCTTCAAGCTAACTCTAATT
TTAAAAAAATCTTCACTTTAAGTAAAGACCCCATTTCCAAATCAAGATTAGTTTAATTAGAAATC
AAAAGCTAGAATCCAATATCAATTTAGCTCTTAAGAATTAGTTACCACAAACTCGA
Done.